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- PDB-6da4: JAK3 with Cyanamide CP10 -

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Basic information

Entry
Database: PDB / ID: 6da4
TitleJAK3 with Cyanamide CP10
ComponentsTyrosine-protein kinase JAK3
KeywordsTRANSFERASE/INHIBITOR / kinase / covalent / TRANSFERASE-INHIBITOR complex
Function / homology
Function and homology information


negative regulation of dendritic cell cytokine production / negative regulation of FasL production / response to interleukin-9 / response to interleukin-2 / response to interleukin-15 / response to interleukin-4 / negative regulation of T-helper 1 cell differentiation / negative regulation of T cell activation / Interleukin-9 signaling / Interleukin-21 signaling ...negative regulation of dendritic cell cytokine production / negative regulation of FasL production / response to interleukin-9 / response to interleukin-2 / response to interleukin-15 / response to interleukin-4 / negative regulation of T-helper 1 cell differentiation / negative regulation of T cell activation / Interleukin-9 signaling / Interleukin-21 signaling / interleukin-9-mediated signaling pathway / interleukin-4-mediated signaling pathway / interleukin-2-mediated signaling pathway / regulation of T cell apoptotic process / negative regulation of interleukin-12 production / interleukin-15-mediated signaling pathway / tyrosine phosphorylation of STAT protein / negative regulation of thymocyte apoptotic process / Interleukin-15 signaling / Interleukin-2 signaling / regulation of receptor signaling pathway via JAK-STAT / growth hormone receptor binding / Signaling by ALK / extrinsic component of plasma membrane / Interleukin-20 family signaling / negative regulation of interleukin-10 production / enzyme-linked receptor protein signaling pathway / T cell homeostasis / cell surface receptor signaling pathway via JAK-STAT / growth hormone receptor signaling pathway via JAK-STAT / Interleukin receptor SHC signaling / extrinsic component of cytoplasmic side of plasma membrane / Interleukin-7 signaling / B cell differentiation / non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity / cytokine-mediated signaling pathway / peptidyl-tyrosine phosphorylation / RAF/MAP kinase cascade / regulation of apoptotic process / protein phosphatase binding / protein tyrosine kinase activity / Interleukin-4 and Interleukin-13 signaling / adaptive immune response / Potential therapeutics for SARS / cell differentiation / cytoskeleton / intracellular signal transduction / endosome / protein phosphorylation / innate immune response / ATP binding / plasma membrane / cytosol
Similarity search - Function
Tyrosine-protein kinase, non-receptor Jak3 / Tyrosine-protein kinase, non-receptor Jak/Tyk2 / JAK, FERM F2 lobe domain / FERM F1 lobe ubiquitin-like domain / JAK1-3/TYK2, pleckstrin homology-like domain / Jak1 pleckstrin homology-like domain / FERM F2 acyl-CoA binding protein-like domain / FERM F1 ubiquitin-like domain / FERM domain / FERM domain profile. ...Tyrosine-protein kinase, non-receptor Jak3 / Tyrosine-protein kinase, non-receptor Jak/Tyk2 / JAK, FERM F2 lobe domain / FERM F1 lobe ubiquitin-like domain / JAK1-3/TYK2, pleckstrin homology-like domain / Jak1 pleckstrin homology-like domain / FERM F2 acyl-CoA binding protein-like domain / FERM F1 ubiquitin-like domain / FERM domain / FERM domain profile. / Band 4.1 domain / Band 4.1 homologues / Src homology 2 domains / SH2 domain / SH2 domain superfamily / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / PH-like domain superfamily / Tyrosine-protein kinase, active site / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-G4V / Tyrosine-protein kinase JAK3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsVajdos, F.F.
CitationJournal: J. Med. Chem. / Year: 2018
Title: Identification of Cyanamide-Based Janus Kinase 3 (JAK3) Covalent Inhibitors.
Authors: Casimiro-Garcia, A. / Trujillo, J.I. / Vajdos, F. / Juba, B. / Banker, M.E. / Aulabaugh, A. / Balbo, P. / Bauman, J. / Chrencik, J. / Coe, J.W. / Czerwinski, R. / Dowty, M. / Knafels, J.D. / ...Authors: Casimiro-Garcia, A. / Trujillo, J.I. / Vajdos, F. / Juba, B. / Banker, M.E. / Aulabaugh, A. / Balbo, P. / Bauman, J. / Chrencik, J. / Coe, J.W. / Czerwinski, R. / Dowty, M. / Knafels, J.D. / Kwon, S. / Leung, L. / Liang, S. / Robinson, R.P. / Telliez, J.B. / Unwalla, R. / Yang, X. / Thorarensen, A.
History
DepositionMay 1, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 28, 2018Provider: repository / Type: Initial release
Revision 1.1May 1, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tyrosine-protein kinase JAK3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,9172
Polymers36,5441
Non-polymers3731
Water32418
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.384, 75.516, 89.621
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Tyrosine-protein kinase JAK3 / Janus kinase 3 / JAK-3 / Leukocyte janus kinase / L-JAK


Mass: 36543.652 Da / Num. of mol.: 1 / Fragment: kinase domain / Mutation: C1048S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: JAK3 / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): SF21
References: UniProt: P52333, non-specific protein-tyrosine kinase
#2: Chemical ChemComp-G4V / (Z)-1-{2,2-difluoro-6-[5-(2-methoxyethyl)-7H-pyrrolo[2,3-d]pyrimidin-4-yl]-2,3-dihydro-4H-1,4-benzoxazin-4-yl}methanimine


Mass: 373.357 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H17F2N5O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.15 Å3/Da / Density % sol: 42.73 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 20% PEG 3350, 0.2M (NH4)2SO4, 2% phenylurea

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Dec 15, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→40 Å / Num. obs: 50218 / % possible obs: 97.8 % / Redundancy: 4.99 % / Net I/σ(I): 25.34
Reflection shellResolution: 2.6→2.64 Å

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Processing

Software
NameVersionClassification
BUSTER2.11.6refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→23.83 Å / Cor.coef. Fo:Fc: 0.8979 / Cor.coef. Fo:Fc free: 0.8852 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.43
RfactorNum. reflection% reflectionSelection details
Rfree0.263 340 4.75 %RANDOM
Rwork0.2271 ---
obs0.2289 7165 97.21 %-
Displacement parametersBiso max: 142.13 Å2 / Biso mean: 50.16 Å2 / Biso min: 12.76 Å2
Baniso -1Baniso -2Baniso -3
1--20.7439 Å20 Å20 Å2
2--11.2262 Å20 Å2
3---9.5177 Å2
Refine analyzeLuzzati coordinate error obs: 0.405 Å
Refinement stepCycle: final / Resolution: 2.9→23.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2215 0 27 18 2260
Biso mean--49.91 38.96 -
Num. residues----281
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d794SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes50HARMONIC2
X-RAY DIFFRACTIONt_gen_planes369HARMONIC5
X-RAY DIFFRACTIONt_it2318HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion276SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2574SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2318HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg3158HARMONIC21.08
X-RAY DIFFRACTIONt_omega_torsion2.85
X-RAY DIFFRACTIONt_other_torsion20.33
LS refinement shellResolution: 2.9→3.24 Å / Rfactor Rfree error: 0 / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.3623 78 4.01 %
Rwork0.2907 1865 -
all0.2937 1943 -
obs--95.06 %

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